Software Engineer at InterMine, in the Dept of Genetics @Cambridge_Uni. Fond of UIs, open source, veggies, running & sci-fi. http://yo-yehudi.com

Jul 28

BOSC 2017 Day 2, Part 3: Keynote #BOSC2017 #ISMBECCB

In which Nick Loman teaches us about making real-world differences to epidemics using genomics, the importance of speedy response to viral outbreaks, and sequencing viruses in the field with no pants. Previous posts: Day 1 of BOSC, Day 2 part 1, and Day 2 part 2.

Nick Loman’s talk was the perfect mix of entertaining humour and uplifting real-world-impacting science. As I mentioned in a previous post, he nearly forgot to provide a title for his talk, which resulted in some gentle, but polite Twitter shaming from the BOSC Twitter account:

Amongst the entertaining responses was Nick’s favourite, “Talky McTalkface”, so without further ado, he got stuck into the talk.

The basic premise of the talk was the fact that viruses can have their genomes sequenced, and when you sequence the virus in enough patients, you are able to trace where the virus came from, and where it has been.

Ebola

Nick’s tale began when Ebola was sweeping through Africa a few years ago. When his team decided to get involved with sequencing the virus, they had a problem: for some strange reason, courier companies were reluctant to ship samples of a virulent, deathly virus internationally. So, after some deliberation, they decided to send the sequencer to the virus, rather than the virus to the sequencer!

Useful results began to pop through after a couple of days, and better yet, another group had begun similar, but less portable sequencing in the neighbouring country of Sierra Leone. Combining the two sets of results (open data sharing!) allowed higher-quality analyses than might have been available otherwise — for example, it quickly became clear from the way the virus lineages were moving across borders that border quarantine control needed to be tightened.

The sequencing eventually allowed the entire outbreak to be traced down to an initial index case. “Patient zero” was probably a child, unlucky enough to be playing near a burnt out tree where they managed to pick up the virus. Whilst the exact animal source isn’t clear, it’s possible it might have been bats.

Given the vast amount of data they’d gathered, visualisation of it was a logical next step for further analysis. NextStrain at the time was focused primarily on the spread of influenza outbreaks, but they expanded their efforts. You can explore the data yourself here: http://www.nextstrain.org/ebola. Useful takeaways from the visualisations include the fact that the virus was primarily clustered in urban centres, and that it would often be exported long-distance to other areas. Nick even mentioned someone who’d survived the virus two years ago, but still had enough viral load to be contagious! (Paper)

Nick also showed us an animation that was beautiful, but staggeringly heartbreaking. It visualised the spread of the disease from location to location, with different colours indicating evolved sub-strains. As pretty as the graph may be, I can’t help but remember that it’s mapping human suffering.

Video Credit: Gytis Dudas/YouTube

A different virus rears its head

About the same time Ebola began to truly fade, a new outbreak occurred, this time in South America: Zika.

Logically, fast response times are incredibly important in terms of preventing outbreaks from becoming epidemics or pandemics. Nick’s team applied for a grant in hopes of heading out to the field to sequence Zika. The turnaround was remarkable — two weeks after the grant application, they had the funding in hand, and were able to set out, as a team, on a South American gene-sequencing road trip.

This time results were a bit harder to get. As Nick explained, when someone is sick with Ebola, their viral load is very high, so sequencing the virus isn’t too hard. By comparison, however, the viral load in an afflicted Zika victim isn’t nearly as high, making results far less useful. Others eventually did have more success with this protocol, sequencing Zika in lab conditions.

Yellow fever and beyond

The rapid action in terms of funding, sharing results openly, and heading to the field all had their part in creating a protocol that was re-usable by others; Nick reported that sequencing of the Brazilian yellow fever outbreak is being managed successfully by researchers, without his team needing to head out themselves.

Wrap up — what a great talk!

Outbreaks are inevitable; epidemics are not — Peter Piot

Sage words, quoted to the audience by Nick Loman. The earlier we get involved in a viral outbreak, the less likely it is to become an epidemic or pandemic. Hopefully, in the future, our viral surveillance will be sufficient that we will be able to prevent further epidemics and loss of life; in the meantime, the work Nick and his team have been performing is truly astonishing, and probably couldn’t have been achieved without open data sharing, swift funding calls, and a dynamite community.

This ends the series of posts I’ve been writing for ISMB/ECCB and specifically the BOSC 2017 COSI. Thanks for reading!

Disclaimer: Any views expressed are my own, not necessarily those of PLOS.